D-I-TASSER Q6X4W1

D-I-TASSER results for Q6X4W1

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: Q6X4W1
Protein Name: NMDA receptor synaptonuclear signaling and neuronal migration factor
Gene Name: NSMF

Input Sequence in FASTA format

>Q6X4W1 (530 residues)
MGAAASRRRALRSEAMSSVAAKVRAARAFGEYLSQSHPENRNGADHLLADAYSGHDGSPE
MQPAPQNKRRLSLVSNGCYEGSLSEEPSIRKPAGEGPQPRVYTISGEPALLPSPEAEAIE
LAVVKGRRQRHPHHHSQPLRASPGGSREDVSRPCQSWAGSRQGSKECPGCAQLAPGPTPR
AFGLDQPPLPETSGRRKKLERMYSVDRVSDDIPIRTWFPKENLFSFQTATTTMQAISVFR
GYAERKRRKRENDSASVIQRNFRKHLRMVGSRRVKAQTFAERRERSFSRSWSDPTPMKAD
TSHDSRDSSDLQSSHCTLDEAFEDLDWDTEKGLEAVACDTEGFVPPKVMLISSKVPKAEY
IPTIIRRDDPSIIPILYDHEHATFEDILEEIERKLNVYHKGAKIWKMLIFCQGGPGHLYL
LKNKVATFAKVEKEEDMIHFWKRLSRLMSKVNPEPNVIHIMGCYILGNPNGEKLFQNLRT
LMTPYRVTFESPLELSAQGKQMIETYFDFRLYRLWKSRQHSKLLDFDDVL

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q6X4W1-D1	1-530	530		MGAAASRRRALRSEAMSSVAAKVRAARAFGEYLSQSHPENRNGADHLLADAYSGHDGSPEMQPAPQNKRRLSLVSNGCYEGSLSEEPSIRKPAGEGPQPRVYTISGEPALLPSPEAEAIELAVVKGRRQRHPHHHSQPLRASPGGSREDVSRPCQSWAGSRQGSKECPGCAQLAPGPTPRAFGLDQPPLPETSGRRKKLERMYSVDRVSDDIPIRTWFPKENLFSFQTATTTMQAISVFRGYAERKRRKRENDSASVIQRNFRKHLRMVGSRRVKAQTFAERRERSFSRSWSDPTPMKADTSHDSRDSSDLQSSHCTLDEAFEDLDWDTEKGLEAVACDTEGFVPPKVMLISSKVPKAEYIPTIIRRDDPSIIPILYDHEHATFEDILEEIERKLNVYHKGAKIWKMLIFCQGGPGHLYLLKNKVATFAKVEKEEDMIHFWKRLSRLMSKVNPEPNVIHIMGCYILGNPNGEKLFQNLRTLMTPYRVTFESPLELSAQGKQMIETYFDFRLYRLWKSRQHSKLLDFDDVL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6003

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	7cpxA	0.34	7.60	0.059	0.557	model1_7cpxA.pdb.gz
2	5u1sA	0.34	7.19	0.039	0.534	model1_5u1sA.pdb.gz
3	5ganA	0.33	7.70	0.051	0.553	model1_5ganA.pdb.gz
4	7nfyA	0.33	7.53	0.061	0.523	model1_7nfyA.pdb.gz
5	7d3eA	0.32	7.41	0.043	0.515	model1_7d3eA.pdb.gz
6	3p8cB	0.32	7.24	0.056	0.504	model1_3p8cB.pdb.gz
7	5h64A	0.31	6.97	0.019	0.479	model1_5h64A.pdb.gz
8	6vz4K	0.31	7.05	0.066	0.483	model1_6vz4K.pdb.gz
9	5f0oA	0.31	7.12	0.045	0.491	model1_5f0oA.pdb.gz
10	6bcuA	0.31	6.97	0.039	0.481	model1_6bcuA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0048306	1.00	calcium-dependent protein binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:2001224	1.00	positive regulation of neuron migration
GO:0010975	1.00	regulation of neuron projection development
GO:0010769	1.00	regulation of cell morphogenesis involved in differentiation
GO:0009987	0.90	cellular process
GO:0080090	0.85	regulation of primary metabolic process
GO:0031325	0.85	positive regulation of cellular metabolic process
GO:0010604	0.85	positive regulation of macromolecule metabolic process
GO:0050896	0.84	response to stimulus
GO:0071371	0.83	cellular response to gonadotropin stimulus
GO:0071257	0.83	cellular response to electrical stimulus
GO:0071230	0.83	cellular response to amino acid stimulus
GO:0048814	0.83	regulation of dendrite morphogenesis
GO:0048168	0.83	regulation of neuronal synaptic plasticity
GO:0043523	0.83	regulation of neuron apoptotic process
GO:0035307	0.83	positive regulation of protein dephosphorylation

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044428	1.00	nuclear part
GO:0043231	0.92	intracellular membrane-bounded organelle
GO:0044444	0.91	cytoplasmic part
GO:0032991	0.91	macromolecular complex
GO:0016020	0.91	membrane
GO:0005634	0.91	nucleus
GO:0097458	0.90	neuron part
GO:0043232	0.90	intracellular non-membrane-bounded organelle
GO:0031090	0.90	organelle membrane
GO:0005737	0.90	cytoplasm
GO:0000785	0.90	chromatin
GO:0097440	0.89	apical dendrite
GO:0045202	0.89	synapse
GO:0043204	0.89	perikaryon
GO:0031965	0.89	nuclear membrane
GO:0030863	0.89	cortical cytoskeleton
GO:0016363	0.89	nuclear matrix
GO:0014069	0.89	postsynaptic density
GO:0005719	0.89	nuclear euchromatin
GO:0005635	0.89	nuclear envelope
GO:0005654	0.74	nucleoplasm

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2e8yA	0.283	6.95	0.039	0.440	3.2.1.41	NA
2	0.060	2fr0A	0.255	6.48	0.023	0.376	2.3.1.94	398
3	0.060	2vncB	0.254	6.47	0.062	0.366	3.2.1.-	NA
4	0.060	1e1cA	0.254	7.06	0.056	0.398	5.4.99.2	NA
5	0.060	1ej6A	0.263	7.30	0.042	0.417	2.7.7.50	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	2y0pB	0.245	7.17	0.027	0.389	0.15	ACO	complex1.pdb.gz	407,408,458,478,479
2	0.01	2vz9A	0.286	7.97	0.035	0.481	0.12	NAP	complex2.pdb.gz	349,350,376,411,412
3	0.01	2xt6A	0.302	6.96	0.050	0.464	0.18	TPP	complex3.pdb.gz	348,349,350,412,413,475

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.